This report is generated by the tcge-cfmedip-seq-pipeline
Selected QC metrics
- NOTE: The heatmap is drawn based on transformed Z scores. In
general, the darker, the worse! Specifically:
- raw_reads_depth, usable_reads_depth, saturation_maxEstCor and
enrichment_GoGe: the darker, the lower
- coverage_pctReadsWoCpG and coverage_pctCpGwoRead: the darker, the
higher
- fragment_size_mode: the darker, the further away from the mean mode
[only for paired-end reads]
Reads QC metrics
Summary statistics for raw, prefilter and aligned reads
- raw_reads_depth: number of raw read pairs [Note: it refers to the
prefilter_reads for single-end]
- prefilter_reads: reads or read pairs after QC, adapter trimming and
UMI barcode extraction (p.r.n)
- mapped_reads_pct: percentage of mapped reads or read pairs over the
prefileter_reads
- usable_reads: reads or read pairs after removing the duplication.
reads pairs require properly paired as well
- usable_reads_pct: percentage of usable reads over raw
reads
Number of samples: 2
| Min |
1400000 |
1399622 |
99.97 |
51 |
92.88 |
100 |
1323813 |
94.56 |
| Q1 |
1400000 |
1399622 |
99.97 |
51 |
93.04 |
100 |
1324792 |
94.63 |
| Median |
1400000 |
1399622 |
99.97 |
51 |
93.19 |
100 |
1325772 |
94.70 |
| Mean |
1400000 |
1399622 |
99.97 |
51 |
93.19 |
100 |
1325772 |
94.70 |
| Q3 |
1400000 |
1399622 |
99.97 |
51 |
93.35 |
100 |
1326752 |
94.77 |
| Max |
1400000 |
1399622 |
99.97 |
51 |
93.51 |
100 |
1327731 |
94.84 |
Usable read depth per sample
Usable read depth percentages against raw read depth per sample
Fragment QC metrics
Fragment size ranges with >=80% properly paired reads
- Calculated by based on PICARD MEDIAN_INSERT_SIZE +
WIDTH_OF_80_PERCENT/2
- WIDTH_OF_80_PERCENT: The “width” of the bins, centered around the
median, that encompass 80% of all read pairs.
MEDIPS QC metrics
Saturation and Coverage Metrics
Number of samples: 2
| Min |
0.98 |
1.27 |
89.68 |
6.590 |
0.57 |
| Q1 |
0.98 |
1.27 |
89.69 |
6.605 |
0.57 |
| Median |
0.98 |
1.27 |
89.70 |
6.620 |
0.57 |
| Mean |
0.98 |
1.27 |
89.70 |
6.620 |
0.57 |
| Q3 |
0.98 |
1.27 |
89.72 |
6.635 |
0.57 |
| Max |
0.98 |
1.27 |
89.73 |
6.650 |
0.57 |
Coverage: percentage of usable reads without CpG, and CpGs without
reads
Enrichment score per sample